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- PDB-2j0o: Shigella Flexneri IpaD -

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Basic information

Entry
Database: PDB / ID: 2j0o
TitleShigella Flexneri IpaD
ComponentsINVASIN IPAD
KeywordsCELL INVASION / SHIGELLA FLEXNERI / TYPE III SECRETION / IPAD / T3SS / PLASMID / INVASIN / VIRULENCE
Function / homology
Function and homology information


effector-mediated activation of programmed cell death in host / extracellular region
Similarity search - Function
IpaD-like / IpaD-like / Type III secretion systems tip complex components / BipD-like superfamily / Type III secretion systems tip complex components / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesShigella flexneri 2a str. 301 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3 Å
AuthorsJohnson, S. / Roversi, P. / Lea, S.M.
Citation
Journal: J Biol Chem / Year: 2007
Title: Self-chaperoning of the type III secretion system needle tip proteins IpaD and BipD.
Authors: Steven Johnson / Pietro Roversi / Marianela Espina / Andrew Olive / Janet E Deane / Susan Birket / Terry Field / William D Picking / Ariel J Blocker / Edouard E Galyov / Wendy L Picking / Susan M Lea /
Abstract: Bacteria expressing type III secretion systems (T3SS) have been responsible for the deaths of millions worldwide, acting as key virulence elements in diseases ranging from plague to typhoid fever. ...Bacteria expressing type III secretion systems (T3SS) have been responsible for the deaths of millions worldwide, acting as key virulence elements in diseases ranging from plague to typhoid fever. The T3SS is composed of a basal body, which traverses both bacterial membranes, and an external needle through which effector proteins are secreted. We report multiple crystal structures of two proteins that sit at the tip of the needle and are essential for virulence: IpaD from Shigella flexneri and BipD from Burkholderia pseudomallei. The structures reveal that the N-terminal domains of the molecules are intramolecular chaperones that prevent premature oligomerization, as well as sharing structural homology with proteins involved in eukaryotic actin rearrangement. Crystal packing has allowed us to construct a model for the tip complex that is supported by mutations designed using the structure.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Expression, Limited Proteolysis and Preliminary Crystallographic Analysis of Ipad, a Component of the Shigella Flexneri Type III Secretion System
Authors: Johnson, S. / Roversi, P. / Espina, M. / Deane, J.E. / Birket, S. / Picking, W.D. / Blocker, A. / Picking, W.L. / Lea, S.M.
History
DepositionAug 4, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_gene_src_variant / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INVASIN IPAD
B: INVASIN IPAD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5893
Polymers70,4962
Non-polymers921
Water37821
1
A: INVASIN IPAD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3402
Polymers35,2481
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: INVASIN IPAD


Theoretical massNumber of molelcules
Total (without water)35,2481
Polymers35,2481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.867, 100.693, 111.993
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.00234, 0.0002), (-0.00234, 0.99992, 0.01279), (-0.00023, 0.01279, -0.99992)
Vector: 56.02134, -0.49937, 98.56983)

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Components

#1: Protein INVASIN IPAD / IPAD / 36 KDA MEMBRANE ANTIGEN


Mass: 35248.234 Da / Num. of mol.: 2 / Fragment: RESIDUES 15-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a str. 301 (bacteria)
Plasmid: PET-15B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18013
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS IS THE N102H VARIANT (FROM PLASMID PMYSH6000 AND PLASMID PCP301). THE HIS IN THE SEQUENCE IS A ...THIS IS THE N102H VARIANT (FROM PLASMID PMYSH6000 AND PLASMID PCP301). THE HIS IN THE SEQUENCE IS A NATURALLY OCCURRING VARIANT

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growpH: 8.5
Details: 25-28 % (W/V) PEG 4000, 0.1 M TRIS-HCL, PH 8.5, 0.2 M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.7→75 Å / Num. obs: 14594 / % possible obs: 90.1 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 8 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 3.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.6 / % possible all: 68.2

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Processing

Software
NameVersionClassification
DMmodel building
SCALAdata scaling
SHARPphasing
SOLOMONphasing
DMphasing
DMphasing
TNT5.6.1refinement
RefinementMethod to determine structure: MIRAS / Resolution: 3→20 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO / Details: REFINED IN BUSTER-TNT BETA 1.9.2
RfactorNum. reflection
Rwork0.235 -
all0.2368 -
obs0.235 12157
Solvent computationSolvent model: BABINET SCALING / Bsol: 145 Å2 / ksol: 0.33 e/Å3
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4422 0 6 21 4449
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00244943
X-RAY DIFFRACTIONt_angle_deg0.5960643
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0041482
X-RAY DIFFRACTIONt_gen_planes0.0096235
X-RAY DIFFRACTIONt_it0.614449420
X-RAY DIFFRACTIONt_nbd0.02716110
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact

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